Other avenues to look at would be adrenal function and gut health. I would recommend the excellent book from Dr Peatfield which talks about the reasons why things can go wrong and what we can do to fix them:

Blood results definitely don't give a full picture. They can hint towards what approach to take, but like you said in the end clinical results are the most important. I totally get where your frustration is coming from, I'm in the same boat!

Have you had any tests for anti bodies? I had raised antibodies (TPO) 5 years after being diagnosed hypo. I was very ill until I started a gluten free diet which reduced the Ab's and I began to feel better.

Hey crimple, how long did it take on gluten free before you noticed a drop in antibodies? I ask because I've been at it for a year but in this time my antibodies doubled from 450 to now over 1000 (don't know the actual number since the lab's range ends at 1000).

I was completely wrong, I was basing what I said off the first set of results, I hadn't read your results properly. Since the second set of results are levo alone your conversion is definitely off. Sorry about that!